Now there are Three
by Sage1988
Summary: AU 'The Sound of Drums'. What if instead of sending the Torchwood Team away, The Master had them arrested like The Jones Family? What secrets would be revealed and why has Gwen got a fob watch?
1. Chapter 1

_This is a story that I came up with about the time 'Last of the Timelords' aired. And before the second series of Torchwood_

_I do not own Doctor Who or Torchwood_

_Enjoy!_

"_Speech"_

'_Thought'_

**Chapter 1 – Another Timelord/Lady**

_**Master's POV**_

'I wonder if I should have sent handsome jack's little gang to the Himalayas? Nah better have them here where I can keep an eye on them'

I sat at my desk and waited. Then a knocking on the door and said "Come on in" grinning from to ear to ear.

A group of soldiers loyal to me came in dragging in four people who despite their struggling weren't going anywhere. The infamous Torchwood 3 team, Gwen Cooper, Toshiko Sato, Owen Harper and Ianto Jones but without their great captain to guide them. They put up quite a fight, taking out seven of his soldiers. But now they were tied and gagged, couldn't have them make a fuss.

Then a separate guard to those holding the captive alien hunters walked in carrying a large box. The guard set the box on my desk and said

"Torchwood 3 neutralised as ordered sir."

I get up and walk around my desk "Well done Sergeant, now what about any strange artifacts in their homes?"

"We searched their homes and found a couple of things sir." He goes into the box and pulled out a spray of Deltan pheromones "We found this in Owen Harper's bathroom" He put it back in the box and then pulled out a Draconian Personal Organiser "We got this from Toshiko Sato's living room" He put it back into box and then got out a Morgo Coffee dispenser that took both arms to hold "Ianto Jones's Kitchen" So that's how he makes the great coffee.

And then the Sergeant pulled out a bomb shell. Not literally but something very shocking. After putting the coffee machine back in the box, he took out a fob watch.

A fob watch with Gallifreyian Markings!

I immediately snatched it out of his hand and used my telepathy to connect to it.

_Mental connection to the watch…_

_I found myself surrounded by golden light and a figure started to walk towards me._

_Eventually the figure came into full view and I saw Gwen Cooper standing in front of me. But the look on her face, one of near arrogant distain and outright dislike._

"_What do you want?" She asked a frown on her pretty face._

"_Well I never thought I'd see you again" I said grinning _

_Then recognition crossed her face "Just get me out of here! NOW!"_

"_My pleasure my dear. My pleasure. But I'll expect a favour in return" I replied, almost giddy at my luck_

"_Fine! Just get me out of here" She snapped _

_Back in the real world…_

I returned to my physical body and crossed the room and stood in front of the gagged Gwen Cooper and slid the gag off her face. She glared and said or rather growled in her soft Welsh tone which made it rather weird sounding

"Who are you?"

"I'm The Master. But the question Gwennnn" I said extending the last sound of her false name "Is who are you?"

"What do you mean?" She asked in guarded curiosity

"This watch is the key to your existence and now its time for you to wake up" I grinned and put the watch in front of her face and opened it

_**End POV**_

Golden light fled the watch into the eyes of Gwen Cooper and her face froze. Then once the light had completely entered her eyes she blinked and her face and eye expression changed to one that resembled a combination of boredom and nonchalance.

"Welcome Back Rani" The Master said and the Torchwood staff faces looked at the person who had been their friend and shuddered at cold look in her once kind brown eyes.

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	2. Chapter 2

**Chapter 2 – The Rani's Story**

_Rani's POV_

Still dressed in a black t-shirt, jeans and leather jacket I sat in a leather seat across from the Master. His smug face made me want to wipe it off his face, but I restrained myself. I might hate him, but I'd promised him a favour in exchange for my freedom from that blasted watch.

I'd been at the fall of Gallifrey when the great world burnt, they'd let me back home to develop weapons for helping fight the Daleks.

The way I felt when the worlds of Gallifrey and Skaro burnt…I couldn't describe it, but the fear I felt…I just ran, and ran and ran. Eventually I landed on Earth in the 1800's and used the Chameleon Arch to hide myself. The identity I took was one Gwyneth, maid for an undertaker named Mr Sneed. But the Cardiff rift locked onto my dormant physic talents and magnified them. To make matters worse I was separated from my watch.

Then the Doctor came and I died in that cellar, but I wasn't a genius for nothing. I'd built a safety system into my Tardis that transmatted me back to my Tardis, resuscitated me, transmatted the watch back and set up a new cover 200 years later, that of Gwen Cooper.

I then became involved in Torchwood and I hoped that my body would notice the watch, but she never did.

So I had to be rescued by the Master of all people, the man I hated completely, my feelings towards the Doctor had mellowed a bit after we comforted each other when our respective children died at the fall of Arcadia.

The war had realised feelings in me, those of compassion, guilt, remorse, regret. All the death I saw…it made me realise how precious life was.

I was still a brilliant scientist, but I now drew the line at something's, like live autopsies or developing diseases to see how bad they got. I'd done a lot of things I'm not proud of.

Now the face of my second body looked towards the man I both hated and although I wouldn't admit it was impressed by. To accomplish what he had was quite good for him.

But back to the present, The Master began to speak "So my dear Rani, I believe you owe me a favour" and I wasn't sure that it was possible his grin widened

I began to speak back "Well get on with it, I doubt I'll like it so let's just get it over with" I snapped

He pretended to look affronted and just laughed "What a mouth you've got my dear" he got up and walked around the table and right in front of me. Quick as a flash he roughly forced his mouth into mine and I pushed him off straight away and got to my feet glaring him at him

He laughed again and spoke in his annoying drawl "You taste as good as you look. Regeneration was good to you. But I'm a married man so let's get down to business, plenty of time for that later" a glint in his eye that disturbed me, I knew a least part of what he wanted. I knew that between the guards and his laser screwdriver I wouldn't have much of choice. I was as much a prisoner as the Torchwood 3 team.

But at least for a while, he sobered up and cracked on "As you know, there might be only three of us left in the whole universe. I want you to change that. I want you to use your brains in genetic engineering and cloning to make a new race of Timelords and ladies to carry on the race and dominate the Empire when it rises"

The task he'd set me was a quite a challenge but I love a challenge and it could ensure the future of our race and it might get him to stop thinking about…that

"All right but I'll need samples of your and the Doctor's DNA and lots of equipment" I said fixing him with an emotionless mask

"You'll have it and plenty of material to work with. But right now you stay where I can keep an eye on you" He said back and he went back behind his desk and pushed one of what I presumed was one of many concealed buttons. Two security guards came in and rather than let them drag me out I got up and walked towards the door they fell in step a short way behind me.

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I HOPE YOU LIKE THIS ONE

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	3. Chapter 3

_Picks up from about when the President was killed in "The Sound of Drums" and the Master just shot Captain Jack_

_This is meant to be third person and bear in mind I haven't seen The Sound of Drums for awhile so the details might be a bit off._

_The will be a quick chapter to start off the Year that Never Was._

_**madeye harry = **__Thank you for giving me the idea about the Cruciform. But I have no intention of letting the Rani or Doctor know but will tell you in this chapter. The Rani's Tardis is on Earth and hidden, but will make an appearance later. _

_And just to let you know if you're reading this I have every intention of continuing all my stories_

**Chapter 3 – The Trinity Together**

As the Martha Jones ran to the fallen Captain, the Doctor yelled for him to stop this and the Master revealed that he'd been behind Trish being at Lazarus's experiment and then proceeded to age the Doctor the Rani was about to enter the room.

It had been two weeks since her return and she'd changed her look. Rather than the predominant black t-shirt and jeans, she now wore a white lab coat, red heels, black skirt and stockings. It was her working outfit now that she was in a lab doing work for the Master.

It made her skin crawl to be even near him, but without her Tardis she couldn't escape. Her Tardis was concealed in a safe place under the best stealth possible, the Master would never find it, but unfortunately until she could escape she couldn't either.

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The Jones family and the Torchwood team were being dragged in by guards and both Jack and Martha looked up in horror at their loved ones predicament.

Jack noticed that Gwen wasn't with his team and a cold weight settled in his stomach.

"Owen, Tosh, Ianto. Where's Gwen?" He asked ash faced

They all looked downcast but Ianto replied "He's done something to her" he thrust himself in the Master's direction but the guard that was holding him pulled him back "She's not Gwen any more"

The confused and very worried Jack froze at the figure coming into the room behind the captives.

It was Gwen

But not the same Gwen Jack was used too

Her outfit was so different, white lab coat, red heels. But the biggest difference he saw in her was in her eyes. The once warm and caring brown that soothed you was now cold and teemed with intelligence.

The Doctor looked at her and his now wrinkled face now registered astonishment

"It can't be" he whispered

"Well it is, isn't it; The Trinity reunited once again, the greatest children of Gallifrey, its best students all in one room" The Master boasted "The Scientist" he gestured by waving his hand in the Rani's direction, "The Adventurer" he moved his arm in the direction of the Doctor "And the Conqueror" he gestured at himself but the Doctor said something else

"No…the Madman"

The Master ignored it and the Rani sent the Doctor a look of what amusement but then when 8:02 came and human things called the Tocafane appeared. Rani remembered how when she'd been a little girl her mother had come and sung to her when she'd been frightened by the Tocafane. But then her mother had died and she'd left in the care of her father, a hard and brutal man, he'd been very violent towards her.

That's why she'd become such a cold scientist. Facts and figures couldn't hurt you. Science was her escape, her refuge and her way of dealing with what her father had done to her. But when the war broke out she'd been forced by the Nightmare child to face those memories, it had been she who'd sabotaged Davros's ship's auto navigation so it would fly into and kill the Nightmare child and Davros both.

She had done many things that made her sick to her stomach. She'd set off a supernova that destroyed the main Dalek shipyards at Kristos Minor, but had also murdered millions of slaves that were held there. With those shipyards gone, they couldn't rebuild their fleet and put the war back years for the Daleks and left them with only a few million ships rather than the tens of millions they had before.

But on another operation in the war, she'd had to go to the Cruciform and destroy the device before the Daleks could use it.

How the Daleks had known about it and how to activate it remained a mystery but they had somehow and stolen it. The Cruciform was a weapon that the Timelords had seized during the Dark times from an alien race whose name was lost to time. The weapon was a space craft the size of an asteroid that had the ability to induce fear within a sentient's mind, such fear that their minds would just shut down and die.

Nightmares that no mind could tolerate and would drive you to suicide to make them stop, There was no known way to shield against its effects and only Timelords with their own telepathy and mental training could stand a chance against it.

She'd seen it used on Polis Optum, when the Daleks had sought to test their new machine. And the whole planet had screamed and killed themselves. After she'd managed to get onboard the floating nightmare and turned it upon the Daleks themselves.

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Little did both the Doctor and Rani know that it was the Master who had given the Daleks the Cruciform in exchange for his life with the intention of taking from them and using it for his own gains. But the Daleks doubled crossed him first and turned the weapon on him. The fear he'd felt made him run to the end of the universe so that the monsters that the device created or unleashed within the Master's mind had not only filled him with fear but made him more insane than ever.

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Rani listened to the cries of all those people, six hundred million, a tenth of the world's population, the cries of those people sounded just like Gallifrey all over again and tears leaked down her face.

She in a daze went about her work, taking samples of the Doctor and Masters DNA to start her work. She added samples of her own DNA as more variety was needed. She knew that to create the race of Timelords she was hoping to make she'd need more DNA patterns.

So her plan was to take samples from the humans and restructure the appearance and family coding of each as many times as possible while replacing everything else with timelord DNA.

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A bit rushed but it's just to get them into the Year That Never Was.

Next chapter you see the Rani start to work and other familiar faces arrive. The Doctor and Jack's reactions are featured.


	4. Chapter 4

_I own nothing_

_And this story is not connected to Prodigy's Journey_

**Chapter 4 – Meeting again**

In a large area on the _Valiant_ which had once been used to ammo store and shooting range by the Unit soldiers, but was now being filled with different pieces of equipment, large vats, hundreds of test tubes, cloning tanks, gene slicing gear, galleons of liquids, and so much else.

In the middle of this mass of technology and chemicals was Rani signing off the list of the needed equipment and having the workers place them where she wanted them and connecting them up to the power supply.

Then a young man entered the room in lab clothes.

"And you are?" Rani asked, not looking up from her and although the young man appeared nervous he replied

"My name Miles Thompson, I've been assigned to help you"

Rani said in a mocking voice "And why would I need help?"

"I'm a skilled mathematician and chemist, with good scores in biology"

Rani looked up to observe her new helper and found a young man of only about twenty, with brown hair and a bit on the short side.

"Really, well I suppose I could use a hand, but in my lab, I'm in charge. Understood?" She said

"Yes Mistress Rani" he said with a slight bow

"Just one question. Why are you here?" Rani asked

Miles looked a bit apprehensive and asked in a quiet voice "With complete honesty, the Master won't hear it? If he hears me complaining I don't want to know what he'd do"

"Yes" The Rani said amused

"I'm immune to the sub wave network, so rather than have me killed as a threat; The Master put me to work. If I don't he'll kill my family"

Rani gave him a look of sympathy and changed the subject "Alright then. Once these vats and tubes are connected up, I want you to create this fluid compound" she said handing him a piece of paper with the formula on it "Then place it in the vats"

"Yes Mistress Rani"

"Just call me Rani"

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Leaving her new lab partner to complete his task, Rani went to collect a few more DNA samples from the Doctor. He was being kept in a tiny tent on the deck of the bridge of _Valiant_. Around the deck there was the Jones Family and Torchwood 3 staff which were chained to the chairs around the table in the centre.

They all looked up to when she came in and both the Doctor and Torchwood team watched her closely.

"Doctor, just a few samples" she said and he offered his arm, rather then have the guards yank it out. She took some blood samples and sick of them observing her all the time

"Alright if you have questions, ask them!" She said in a resigned voice and the Jack asked angrily

"What have you done with Gwen?"

Rani let out a sigh "Nothing, she was just a disguise, an illusion, she ceased to be when I returned, and this is my body!"

Jack looked deflated and the Doctor took his turn

"How did you survive?"

"I was delayed for the final battle by Dalek scout ships. I arrived to see Gallifrey burning, to hear all those burning" she said and anguish broke free on her face "I was so scared, so much death…I just ran and ran…made my self human so no one could find me" she said and shook herself to regain her composure

"So now you're working for the Master" the Doctor said with distain

Rani snorted in disgust "You think I want to be here! Forced to work for that maniac! Either I create a new generation of Timelords or he rapes me, to make them naturally!" she said angrily and the shock on their faces was apparent "What I'm a female, he's a male, we're unrelated and we are both fertile"

"I can see the position your in" the human know as Owen Harper said and she sent a look of at least relief that someone did

"Now I need some samples from some of you as well" Gwen said after storing the samples that the Doctor had given safely.

"Why?" Tosh asked, still upset that her best female friend had been 'taken over' and destroyed by an alien

"To make the new DNA codes I need as many suitable patterns as possible. Just a couple of blood samples that's all" Rani said and took a few samples from around the room

"How do you plan to do it?" Doctor asked interested in how she planned to resurrect the Timelord race

"I take the DNA samples I've collected and clone them. Once I've made as many as possible, rearrange the genetic code to create a totally pattern, mixing the human DNA with Timelord genes eliminating the human traits so to create pure Timelords" Rani said looking him in the eye and giving a smile. If there was a subject he and the Rani could go on endlessly about, it was science. He started to smile too.

"That's impossible, you can't just rearrange DNA like that" Owen Harper said

"For your backward race yes. Not for us. We were doing more complex feats before your planet came to be" Rani said with distain, she still looked down at humans. But then the Doctor did sometimes.

"If anyone can she can. Rani's the greatest mind Gallifrey's produced since Rasillon and Omega" and the Rani's grin returned.

"I noticed you've got a new companion" Rani said observing the Doctor for his reaction.

"Yes Martha" he said and Rani noticed the faraway look in his eyes and the pleasantness in it.

"So you love her don't you?" Rani said and the Doctor gasped too quick to deny it

"No, no, Martha's just a friend"

"I think you do. I think that you love her so much that you pretend that you don't notice how she looks at you" Rani growing surer of her diagnosis

"Why does he pretend not to notice?" Francine Jones asked she didn't like that he was playing with her daughter's affections.

"Because every time he's loved someone, they've been taken from him" Rani said with sympathy, she'd felt this pain herself "His wife, his children, Miss Tyler" the Doctor's head fell

"I know it hurts Doctor, but deny what your hearts tell you is to deny life, to truly live. When you see Miss Jones next, tell her how you feel" She said looking him straight in the eye.

Then she gathered up her samples and left to return to her laboratory

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Meanwhile in the remains of a street called Bannerman Road, Martha was getting supplies and some clothes from a woman she'd met named Sarah Jane Smith. Apparently she'd also travelled with the Doctor and was starting a resistance to fight the Master. She was an alien hunter and with her own small team of two teenage boys called Luke (her adopted son) and Clyde and a girl named Maria.

When Martha had told Sarah Jane about the plan the Doctor had devised and she had pledged her support. She was getting Martha food, water, and clothes so she could begin her journey, and providing her with moral support.

And with her backpack ready Martha was bidding farewell to her new friends.

"You're sure it's alright?" Martha asked, Sarah Jane had not only put herself at risk by harbouring her, but had given her alien tech to help her against the Master. No weapons, but some useful items, like her spare sonic lipstick, a scanner watch like hers, vorgatt defence field emmiter, an antigravity harness that would help her with climbing and a position locator programmed with up to date maps of the Earth so she could always find where she was. As well as food, water, maps, spare clothes and other essentials.

"Oh course Martha, what your doing is far too important. I've met the Master. I know what he's like"

And giving her a smile the younger woman set off along the back streets.

An hour later a helicoptor appeared and landed at the end of Bannerman Road with a dozen Toclafane and a few armed guards around it.

Then the Master got out and the guards and Toclafane forced people to line up along the street and waited behind them.

The Master walked slowly up the street and started talking

"My dear people, one of you has been very naughty, harbouring Miss Martha Jones. She may be gone now but I must find the perosn who fights me. So who is it?"

The people in the street lowered their head and stayed quiet and then the Master noticed Sarah Jane.

"So the old girlfriend. Well this is a turn up for the books and answers my question as to who was hiding Martha Jones"

Sarah Jane's head rose to meet his gaze "Yes, I remember you The Master and I know that you will be stopped"

The Master gave a chuckle and said "Yes but it won't be by you and it's time to teach those children of yours a vital lesson" He paused and the Toclafane swarmed around him "Everyone dies" and he turned to the floating orbs around him "Kill her"

And the orb fired its powerful weapon blasting Sarah Jane into pieces!

For a brief moment there was a shocked silence which was broken by Luke yelling "I'LL KILL YOU! I'LL KILL YOU!" he was restrained frm running at the Master and being blasted to bits by Paul Jackson and Clyde Langer. Maria was crying and shooting glares at the Timelord while Clyde was shedding his own tears and restraining himself from running at the Master who was laughing

Just Laughing till he sobered up a bit while people gave him looks of disgust.

"I think I need to keep an eye on these children. Take them to _Valiant_"

"What…get off…let them go" cries went around as people tried to protest as the teenagers were pulled of by the guards struggling against the guards dragging them away, while the adults were held back by guards and the Toclafane firing a few warning shots and spinning their blades.

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After the children and the Master were gone, the Toclafane fire bombed 13 Bannerman Road, reducing it to ruins.

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When the Master and his captives arrived back on the floating airfield, he went to his bedroom to have a nap while his young captives were thrown into the prison cells that had finally been readied with the Jones family and Torchwood team.

They just sat as tightly as they could to each other with out sitting on each other. Sarah Jane was always the one to have a plan, to know what to do. Without her they were lost, not ready to go it on their own.

After an uncomfortable half an hour Clive Jones approached them

"I'm Clive. What are your names?" he said as friendly as possible

"Luke"

"Maria"

"Clyde" they said and looked despondent

"What happened?" he asked dredging the answer

"He murdered my mum…Just had her shot. And then he just laughed, He laughed" the boy who called himself Luke said and broke down into tears and the girl calling herself Maria pulled him into her arms and he wept into her shoulder as she wept herself. The boy named Clyde wrapped them both in his arms and joined them in their sorrow with his own tears.

Everyone was shocked, every time they thought the Master could go any lower he did. Having the a boy's mother shot in front of him and then just laughing at it…he really wasn't…wasn't human, they all thought. And while he really wasn't human, it just made them sick to their stomachs.

"What ever it takes I'll kill him. I swear I'm going to kill the Master" Luke growled, his sorrow replaced with anger. And the other two nodded their heads

"Together Luke, we'll get him together" Clyde said putting his fist out in front of them. Maria put her own fist next to it and Luke added his own as they united their pledge.

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_Two weeks later…_

Rani sat in her lab looking over the test results of all the people onboard and looked at which DNA patterns would be useful in her experiments.

Trisha and Clive Jones were good choices, as were Maria Jackson and Clyde Langer. Toshiko Sato was the only one out the Torchwood staff, the Doctor, the Master and herself of course. Six of the guards on the ship, a UNIT soldier that was onboard called Ross Jenkins, a journalist named Julia Swales who was arrested after helping Martha Jones get a boat so she could cross the Atlantic Ocean, Luke Rattigan a boy genius that was with his father an ambassador during the supposed meeting with the Toclafane, Penny Carter a medical student who had killed several guards while posing as a medic and was arrested for questioning, and Sally Sparrow a human that the Master had arrested for leads to Martha's location.

He arrested anyone that had any potential information on the young woman's whereabouts; he was obsessed with finding her.

Rani had enough material to create 200 new Timelords by reorganizing each DNA code 10 times. Then growing the sample into an infant in pods that she'd modify to act as an artificial womb.

Miles was working on pods and the monitors, while she did the genetic work.

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_Please remember this is the Year that Never was, so when the Paradox machine is destroyed Sarah Jane will be brought back_

_I probably got the dates wrong for Sarah Jane and her crew to be in this but for my story they are_

_Please Review!_


	5. Chapter 5

_I own nothing_

_A little something for Deadeye 86, thank you for your review, hope you like it if you're reading_

_Thank you also to madeye Harry for reviews_

**Chapter 5 – Experiments**

Rani sat in her lab securing the DNA samples in their pods so that they could be placed into the now named gestation pods where the samples would be grown into foetuses and then into infants where they would be born and be raised. She didn't think she was up to the task of trying to raise 200 Timebabies on her own but she'd find a way.

Miles, her new assistant was sorting the records of her experiment into an order that made them easy to find. The young man had proved useful in monitoring the processes of the gestation process. He had a surprising intellect for a human and she felt her might have some worth.

Mid morning when she was securing pod 165 properly a burly guard appeared flanked by a metal orb that called them selves the Toclafane.

"The Master has ordered you to the main deck for a report on the cloning of the new Timelords" the guard said clocking his rifle

Rani signed and called "Miles" the young man went over to his boss and she continued "Check that all the seals on the pods are secure and they have the correct amounts of each fluid. Check the other pods for levels" Miles nodded and went do his new task as Rani was led away by the two stooges of the Master.

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The Main Deck was as normal but had "I can't decide" by Scissor Sisters playing in the background as it did every morning with the Master spinning the Doctor around on a swivelling chair so fast that the Doctor could be sick.

He stopped after 10 minutes and the Doctor just sat back and wheezed, his eyes spinning and Tisha Jones now acting as a maid looked up concerned for the old man but knew not to run over, for all the trouble it would cause.

But the Master turned to face Rani and grinned a cheesy grin "My dear Rani" he said, crossing the room and taking Rani's hand to give it a peck of the lips making her skin crawl "Your work on the new Timebabies has been astounding but now I need you to do something else for me"

Rani was immediately suspicious "What exactly is it your want me to do?"

The Master replied "I need you to come up with a way to turn human into a Timelord without the weeks of successful gene therapy. I want my Lucy to join me watching the Empire for centuries, not her too few years" he said motioning towards Lucy who smiled but there was a black eye. Clearly she was being abused but she was too in love with the Master to realise it yet.

Rani crossed her arms "You want me to turn a human into a Timelord in days rather than the weeks it would take to be done safely"

"Not days…hours" The Master said coming up with a real humdinger

"HOURS! TO DO IT THAT FAST IT WOULD ALMOST CERTAINLY KILL THEM!" Rani shouted, he knew that as well as she did that changing a genetic code that fast was sure to cause genetic instabilities that could easily be fatal.

"You'll just have to find a way won't you?" The Master grinned, untouched by her declaration and with that he went to sit in his chair for a massage and Rani was led back to her lab

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Rani was sitting at her desk trying to think how in Rasillon she was going to do this? Altering Genetics to change an entire code was very difficult and down right dangerous. When she was creating the Timebabies, all she'd done is extracted the human strands and replaced them with Timelord ones with it being in a sample and not a living being yet it was not likely to suffer and die.

Gene therapy was a slow process where a piece at a time the structure was changed to allow the body to cope with the changes. To do it so quickly was going to shock the body into shutting down.

Then she thought of the way an organism consumes food or what ever it depends on and then converts it into fuel for itself and then she got a blast of inspiration.

A virus that would go through the body and consume the human DNA strains and then excrete the Timelord genes; then the virus when it had no human DNA to consume it would die out and shun the brain into a short term coma so that it didn't shut down and could grow used to the changes.

It would be difficult to engineer and then would require tests but it was possible.

So she called Miles over and they got to work

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Over the next couple of months of Rani and her young assistant managed to engineer a virus that did exact what Rani had envisioned and tried it on a small scale with human cells.

But now was the time to test it on an actual human being. The Master would not dare risk Lucy in a dangerous trial like this, so he had sent Rani a prisoner from the cells to try it on.

A human female named Sally Sparrow

To say that Rani was nervous would be an understatement. This virus was very experimental and this was the first time it would be used on a living human, who knew what would happen. There was likely to be great pain and for her own safety she would be restrained upright.

The young blond woman was dragged in and strapped to the table, all the while struggling, but futilely.

Rani said once the big men had secured the young woman "Leave us. I need my space" and rather than question her, they left.

The young woman looked afraid, no-one had told her what to expect and now she was strapped to a table of a laboratory

Rani stroked her head in a soothing motion "Sally" she said trying to relax her "I sorry to have to expose you to this, but if this experiment works you'll become far more than human. You'll become a Timelady, like me" she said letting the information sink in while still stroking the blond head of the young woman.

"Like you. But I'm human, that's what I was born as, that's what I want to be" she said a little agitated but Rani was using her telepathy to calm her.

"I'm sorry, but you and I have little choice in this. I have to warn you, there will be great pain, but then you'll wake a new woman" and without warning she injected Sally Sparrow with the Timelord virus.

The shock lasted only a couple of seconds before the screaming started. Sally trashed about as her insides were restructured to change her into a new Timelady and after a minute she suddenly fell silent.

Rani stroked her head once again before going to the monitors to check the young woman's read outs. The rate of change was astounding, a second heart had grown, her circulatory system had been restructured to accommodate the second pump, and her brain's psychic centres came to life.

As the night waned on, Rani kept checking the young woman's vitals to make sure they were stable and her new body was functioning perfectly, with no sign of rejection or collapse. There was no trace of human DNA left in the young woman's body.

'I'll take care of you' Rani Thought as she stroked Sally Sparrow's face 'I'll teach you all you need to know'

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After a few days analysis it became clear that the experiment was a complete success, the Master was so pleased that he allowed Rani to keep Sally as an assistant and student.

A week later the young woman woke to discover herself changed and with a degree of freedom. At first she was adamant that Rani turn her back, but broke down when it was explained that that was impossible and had to be consoled by Miles since Rani thought to give the younger woman space.

That was also the week that the entire island of Japan defied the Master and shielded Martha Jones. The Master was not impressed and made the entire staff of _Valiant_ stand on deck as the Toclafane fire bombed the entire country, killing all those trying to escape. There wasn't a dry eye on the deck except for the Master and his whacked out bride.

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_Hope you enjoyed the chapter _

_PLEASE REVIEW_


	6. Chapter 6

_I do not own Doctor Who or Torchwood_

_Thanks to everyone who has reviewed, much appreciated _

**Chapter 6 – Figuring things out**

The Doctor was staring out of a portal on the main deck of the _Valiant_. The flying spheres that the Master had named 'Toclafane' flew past as they did everyday as part of the defence of the flying aircraft carrier.

He pondered as he often did these days as to how the Master had recruited the Toclafane in the first place, and then maybe he could figure out someway of dealing with them.

Like Hercule Poirot, he looked at the pieces of the puzzle that he had;

_The fact that the Tardis could only travel between early 21__st__ century Earth and the end of the Universe_

_The name Toclafane which came from his own people's mythology and didn't exist in both the time frames that the Tardis could travel too_

_The paradox machine that would allow altering the timeline _

_And finally that the Toclafane could only come in full force when the paradox machine was activated_

So this meant that the Toclafane must come from the end of the Universe, because that was the only place that the Master could go with the Tardis. But why the Master would need a paradox machine for them to exist?

Answer if the Toclafane had some connection to now Earth and their actions would affect their own future, the Paradox machine would prevent them from being affected.

Then what could be there connect to Earth of now be?

And his great brain figured it out almost immediately

"No it can't be"

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Toshiko Sato dressed in white chef's outfit, in the kitchens chopping tomatoes. All of those the Master had brought aboard but a dangerous few were put to work.

Owen, Ianto and Clive Jones were out to work as cleaners, while Francine and Trisha were used as maids.

Jack and the Doctor were too dangerous to be let around so they were always under watch or locked up or both.

Tosh on the other hand had been assigned Kitchen duty, several times she had been tempted to slip something poisonous into the Master's food, but the food was always scanned by the Toclafane before it was consumed so any attempt to kill the Master via food or drink would be detected. The last cook who tried…

His screams had been awful; the sick bastard had had them broadcast over the PA system, for two days and made the crew line up one by one to look at what was left of him.

Let's just say that there were quite a few bloats of vomiting, tears and nightmares.

So everyone just cowered and prayed that someway, somehow the Master would be defeated.

Some took more active roles in the defeat of the Master, like the Jones family and the Doctor. Owen and Ianto helped but Tosh herself was to far removed to be of any help.

Today she had received a surprise; she was now the cook for the research staff, in other words The Rani.

She would take the food to her and her staff themselves after she had prepared it. There were only three of them so it wasn't too much of a work load increase.

The hard thing about it was seeing that alien, the same species as the Master, in Gwen's body.

She didn't believe that Gwen had just been an illusion, the woman that had been her best friend, was too human. A kind warm and caring person, a person that despite the world in which they lived kept her conviction that Torchwood was there to help the world.

She finished the food of the day; Chicken Vindaloo. One of the Master's favourite foods, and his tastes decided what everyone ate.

She placed the three dishes on a tray and started to wheel them out of the Kitchen towards the labs followed by the Toclafane, who scanned the food to make sure that the food was safe. The Rani was too important for the Master to risk.

She soon arrived at the labs and the security guards scanned her with all manner of devices and finally let her in.

The sight of a lab made her think of the better times in Cardiff and the Hub.

She missed those times, where she and her friends would unravel the mysteries of the universe and defend the world from aliens.

The Rani didn't seem to be around, but her assistant and new pupil Sally Sparrow where. They were attending to pods that were shaped like a sphere about a metre and a half across with various small monitors attached to each one.

"Hey Tosh" Miles said with a smile "Chicken Vindaloo delicious" he said when seeing what delights she had brought them today with not a little sarcasm

At least no-one staved on the _Valiant_, unlike on the planet below. The Master wanted his personal slaves healthy…all the better to torture them and break them when they were strong. It was delightful for the Master to see someone break, more of a challenge. According to hi it was too easy to break a weak and staving person.

"What's going on?" she said looking at the pods. The last time she had been allowed inside the lab, rather than just passing the food through, they had been to busy to answer any questions.

"The Gestation and Incubation Pods had to be checked for progress in the growth process" Sally answered; the young lady had found her new skills developing under the Rani's tutorship.

"How long before their born?" Tosh asked peering into the little viewing port

"About a year and a half" Miles answered

"Why so long?" Tosh asked

"Rani says that Timelord pregnancies last about 10 months but that reason for the extra time is that Rani is going to accelerate their growth to about 2 years old when their ready and that will take a few months to be safe" Sally explained

"Where is the Rani?" Tosh asked looking around as if expecting to see her

"Called to make a report to the Master" Miles said with concern

Tosh nodded and then by unbelievable coincidence, in walked the Rani, wheeling in the Doctor who was bound to a wheelchair.

Miles and Sally jumped to their feet and stood as if to attention and the Rani ordered

"Go through to the office and take Miss Sato with you, take the food"

"Yes Rani" they said and pulling the tray with them, crossed the large lab and enter the small cabin that had been converted into an office.

Leaving the Rani and Doctor alone

"Right let's get you scanned and check that the Master hasn't done any other damage than the obvious" the Rani said moving him to the centre of the room where a scanning unit that looked like a spotlight connected to a computer sat.

"Right let's do this" the Rani said turning on the unit which traced the Doctor's frail body and the console beeped. The Rani went to the console and checked its findings

"Everything seems alright, just the classic signs of aging, less muscle tone, decreased vision, decreased hearing etc. How do you feel?"

"Considering everything that the Master has done, ok; he doesn't want you or me dead or injured. If we were, we'd be useless to him" The Doctor said

"All ready figured that out. What use is killing us, when he can force us to admit his superiority? For us to bow to him" The Rani said too which the Doctor only nodded

She pulled the chair out from behind the scanning unit and placed in front of the Doctor and sat opposite to him.

"We haven't had a chance to talk since the Master took power. So let's talk" The Rani said leaning forward in her chair

"What about?" the Doctor asked wearily

"Susan, I believe that is what you called her. A better cover name than Doctor" The Rani said, the hard look in his eyes told him he couldn't get out of this one

"I don't know how she is. She fell in love with a human on Earth in the 22nd Century. I respected her choice" the Doctor said avoiding her gaze

"And you didn't check on her?" the Rani said in a low but dangerous tone.

"No I always meant to go, but I never had the time" the Doctor said lamely

"You are nearly a thousand years old, spinning through time and you say you've never had the time!" The Rani said getting a little angry. The Doctor had simply never bothered at least in the Rani's eyes to check on the mutual granddaughter. The Rani would have gone looking for Susan herself, but she didn't know where the Doctor had left Susan.

"I know its irresponsible but I don't do domestic. I can't handle those situations" the Doctor said to defend himself.

"Well I'm sorry that your only grandchild caused you so much annoyance" The Rani said bitterly and looked away from his face; the Doctor's face looked both guilty and uneasy

"I'm sorry, but I' am who I' am" the Doctor said trying to say something "And knowing you, you probably found a way to stop the Master" trying to change the subject

The Rani looked up to meet his eyes and said "Likewise, I know that Miss Jones was given a mission to stop the Master"

"Perhaps" the Doctor said not trying to give anything away

"Your physical is done" the Rani said "I'll call some guards to take you back to the Bridge, I've got work to do" and with that she headed for the office to call the Bridge

Leaving the Doctor alone to think

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Meanwhile on the engineering decks two young men were whispering to each other

"Maria got duty as the maid for this level. Tomorrow we go" Luke quietly said to his friend

"I just hope that this plan works Luke" Clyde replied in an equally hushed voice

"It has too" Luke said and the two continued to mop the deck, knowing that either they would manage to get their revenge against the Master, or they would be dead

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	7. Chapter 7

_I do not Doctor Who, Torchwood or Sarah Jane Adventures_

**Chapter 7 – A plan**

Luke Smith crawled through maintenance shafts on _Valiant_ trying to reach under the main deck. He was setting the electrical lines under the deck to detonate a power conduit and take out the table area of the main deck and hopefully the Master with it.

Clyde was keeping an eye out in the corridor; Maria had been observing the Master while working on the main deck so to try and find out when he was sitting at the table so they knew when to detonate their makeshift bomb.

They had found that from 10 am to 12 am the Master sat down to have a massage and then work on his plans for universal domination. That when they were going to detonate their bomb.

_1 hour from now…_

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The Master was just waking up from his slumber and looked over to his wife Lucy who was still sleeping peacefully, her face marred by the bruise forming around her eye. She had objected to him feeling up the massage girls but soon she was the one apologising when he had 'disciplined' her.

Either way he got up and dressed in his suit and left the room heading straight to the main deck for his morning coffee and massage.

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_30 minutes…_

Maria was standing on the deck pouring out the coffee for the Master, they never knew when he would get up in the morning so they had to pour a new one every hour. This morning there it seemed he wasn't to wake until 12 o'clock so this had been the 4th serving.

This morning Maria was on main deck duty with Tisha Jones and a woman named Alicia Brant, a journalist who had been covering the first contact and was now like the rest of them a servant of the Master.

The Doctor sat up in his little tent like dog house, her heart went out to the man that was being treated as less than an animal; the man that Sarah Jane had talked about and admired so much.

It was the practise of the maids to sneak the Doctor and bit of food and tea. The Master for his own humour had decided to feed the Doctor nothing but dog food and water in a bowl. There were rarely Toclafane on the deck and the guards hated the Master as much as the rest of them did so the guards turned a blind eye. They were kept in fear of their families being murdered by the Master but would try to resist him in any way possible.

She was keeping as far away from the table area as possible while trying to make it look as if she wasn't.

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_25 minutes…_

The Master entered the deck playing yet more tracks from his favourite Scissor Sisters album, by this point everyone had developed a great but quiet hatred of the Scissor Sisters, why hate because they had listened to the same tracks over and over again, and quiet because if anyone said anything about it, the Master had them put on extra loud earphones that played the Scissor Sisters so loud it burst their ear drums.

He got the Doctor into a wheelchair and started to spin the Doctor around and around in the wheelchair, laughing insanely.

The guards and maids were queasy just watching, but the poor Doctor looked like he was about to be sick.

But after the Master had finished laughing he sat down at his desk, drinking his coffee and looking through his plans to conquer the universe, reports on the rockets construction and rebel activity reports.

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_5 minutes…_

The Master was sitting back in his chair watching an episode of the teletubbies, marvelling at the show while everyone ignored it and went about their work.

Maria was now about to go back to the cells for her sleep time when the Master ordered

"You" pointing at Maria "Another coffee"

Maria quickly made her way to the coffee machine and started to make the coffee he preferred it, five sugars with plenty of milk.

The machine was agonizingly slow to get going and the Master kept clinking his fingers a sign that showed he was impatience and Maria rushed to get the coffee prepared.

The bomb could go off any time now.

She moved to deliver the coffee to the Master but out of patience he got up and went to collect the coffee himself.

Maria's heart sank

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Just as the Master reached Maria, the bomb went off; the entire table area exploded sending everyone to the ground, the explosion was too localised around the table to take out the whole deck.

Immediately the Toclafane swarmed around the deck and the Master got to his feet.

His face was horrifying to look at; it wasn't damaged from the explosion but the look of fury was so frightening to look at.

His gaze went to Maria who was too stunned to move or speak; he grabbed her by the arm and placed his hand very roughly on her face.

He used his telepathy to ripe into her mind, this was not gentle, to Maria who immediately became aware, she screamed as the Master shredded her mind, it felt like your hand was being torn apart in front of your eyes.

He soon found the information he was looking for and threw her to the floor, Maria curled up into a ball and sobbed, the pain was so great, and every bad moment of her life was flashing in front of her eyes.

In the following hour Clyde and Luke were 'questioned' and admitted to everything, the three of them were then executed by disintegration.

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_Please Review_


	8. Chapter 8

_I do not own Doctor Who_

**Chapter 8 – A plan in motion**

A week after the three teenagers were executed, it was time for Lucy Saxon to step into eternity.

She was strapped onto the table and waited impassively, the Master stood off to one side grinning, while Rani prepared the virus injection.

"Right the injection is ready. Could you please leave the lab?" Rani asked turning towards the Master whose grin faded

"Why should I? This my wife" he said

"Because this is a small area and I need to keep monitoring her, your just going to get in the way" Rani said with a glare

"Fine but if she dies…" the Master warned and with that left without a backward glance.

Lucy watched him go with sadness and Rani while used distraction to inject Lucy with the virus.

As with Sally there was a moment of shock before the pain started and Lucy started screaming

* * *

Over the next 24 hours the process was completed but Rani still had one thing left to do.

She placed her hands on the sides of Lucy's head and concentrated.

* * *

Martha meanwhile was walking across America, at the moment she was crossing the Rocky Mountains.

It was late summer getting into autumn and the temperature was slowly starting to drop. She was camping at Moraine Lake which was one of the most beautiful places she had ever been. Although there was a nearby village the lake itself was untouched

The snowy mountains stood tall and mighty, the lake pure and clean surrounded by trees that were still green.

She had taken this short break in travelling to recharge her batteries and rest up. She also refilled her canteens of water. She was swimming when doubt struck her

'What if I fail? What if I can't do what the Doctor asked me to do?' she thought as she got out of the water and towelled her self dry.

Then almost as if he was here with her she heard the Doctor's voice in her mind

'You can do it Martha. You're already doing it' his soft tone wrapped her in a proverbial blanket of warmth and reassurance.

She smiled and got her jumpsuit back on

* * *

On the bridge of the _Valiant_, the Doctor smiled as he felt her become a bit happier. Martha thought it was her own imagination instead it was the Doctor projecting his thoughts to her through the psychic network of Archangel Network.

* * *

Rani watched as the Master embraced the new Lucy and inwardly she grinned

'The last piece is now in place, now to wait for the right moment to strike'

* * *

_The next chapter is the Last of the Timelords and a big one in terms of the story so I didn't want to give much away_

_Please Review and tell me what you think_


	9. Chapter 9

_I do not own Doctor Who_

**Chapter 9 – Last of the Timelords**

It had been nearly a year since the Master had taken power and the _Valiant_ was gearing up for the launching of the rockets armed with black hole converters.

The Master was meanwhile walking into the lab where Rani was working on the new Timelords, she had been quiet recently and he was bored, so he decided to pay her a visit.

He found her inside sitting at her computer typing up notes on the progress of the babies, he walked over to her but she didn't divert her attention away from what she was doing. He sat on her desk and said lazily

"What you doing?"

She responded without looking up and kept on typing "Working"

"Well" he said snatching the keyboard away from her to get her full attention "Let's talk awhile" he grinned

She looked at him annoyed before signing in defeat "Ok, what do you what to talk about?"

"Well I just think I should congratulate you on your stellar work. After all you did all this with such primitive equipment" He said gesturing around them

"Appreciated, now do you really intend to use those black hole converters?" she asked

"Of course, one in enough to devastate a whole solar system" he said grinning

"Are you nuts? With that kind of weaponry no space going race with leave Earth intact. If they don't come along to steal the converters they'll band together and destroy Earth" Rani raged getting out of her chair quickly

"Not with an effective first strike" he said

* * *

Rani knew better than to argue the man wouldn't know sense if he was right up close to it. Both she and the Doctor had plans to break the Master's power and though she couldn't be sure, she had pretty much figured out what the plan was and it would work with her own.

All the pieces had been put in place some time ago.

* * *

The Doctor's attempt to steal the laser screwdriver went badly and now he was reduced to a small pigmy creature. Rani looked at him with sympathy and in her mind was already trying to devise a method to restore him to his former self. She walked up to his cage and said "I'm sorry, I will fix this"

"I know, we'll both fix this" he said back in his gravely voice

At that moment the Master came into the room accompanied by Lucy, sporting a new black eye. The Doctor and Rani turned to face him and glared

"Tomorrow they launch" he said with Lucy on his arm, he shook it off and came nearer "We're opening up a rift in the Braxatolion space, never see us coming. Kinda scary"

"Then stop" the Doctor said

"Once the Empire is established and there's a new Gallifrey in the heavens maybe then it stops" the Master said in response and he walked closer to the cage. Rani stepped forward between the Doctor and the Master as if to shield the Doctor from him

The Master ignored her and said to them both "The Drumming. The never ending drum beat" he paused and then continued "Ever since I was a child, looking into the vortex, that's when it chose me, the drumming the call to war. Can't you hear it?" he asked honestly surprised they couldn't "Listen its there right now" he looked to the Doctor and then Rani "Tell me you can hear it Doctor? Rani?" he asked "Tell me?"

The Doctor leaned against his cage "It's only you" to which the Master responded "Good"

"We are all different we three" the Master said backing away from the cage "The Doctor when he looked into the vortex, he ran away in terror. Rani who looked and was inspired by its power and majesty and me who was chosen by the drums"

But their conversation was interrupted by the arrival of a Toclafane "Tomorrow the war, tomorrow we rise, never to fall" and landed on a small rod that emerged from the table

"You see, I'm doing it for them" the Master said gesturing to the Toclafane "You should be grateful, after all you love them, so very much"

He sank into a chair and told them how he recruited the Toclafane "I took Lucy to Utopia, the Timelord and his human companion" he said turning to face Lucy "I took Lucy to see the stars."

"Trillions of years into the future, to the end of the Universe" She said in a sort of mixed voice of awe and horror

"Tell him what you saw" the Master told her

"Dying, everything dying. The whole of creation was falling apart and I thought there was no-point. No point to anything, not ever" she said

"And it's all your fault" the Master told him but Rani surprising even herself jumped to his defence

"This is no-ones fault but the humans, they chose it"

"Oh you should have seen it though" the Master said pretending as if she had never spoke "Furnaces burning. The last of humanity screaming at the dark. All that human invention that had sustained them across the eons, it all turned inwards. They cannibalised themselves" he said while Lucy looked at the Toclafane with revulsion

"We made ourselves so pretty" the electronic childlike voice of the Toclafane said

"Regressing into children, but it didn't work. The universe was collapsing around them" the Master said and the Toclafane said "Then the Master came in his wonderful time machine, to bring us back home"

"The Paradox Machine" Rani said

"Oh my masterpiece" the Master said proudly "A living Tardis strong enough to hold the paradox in place, allowing the past and the future to collide with infinite majesty"

"But your changing history" the Doctor said struggling to get up "Not just Earth, but the entire universe"

"I'm a Timelord, I have that right"

"But even then" the Doctor said "Why come all this way just to destroy?"

"We come back, to build a brand new empire, lasting a hundred trillion years" the Toclafane said and the Master added "With me as their Master. Timelord and human combined haven't you always dreamed of that Doctor?"

"Not like this" the Doctor and Rani added her own two cents "This will only end badly"

The Master then rose from his chair and said "Human race the biggest monsters of them all" before leaving with Lucy in tow

* * *

That morning they all gathered on the main deck, the Jones family, Jack, Owen, Tosh and Ianto. The Rani with Miles and Sally and the Doctor alongside the Master and Lucy to observe what was to be Martha's execution

They all looked at the sombre young woman and gave what looks of encouragement they could

Once Martha had walked to the foot of the stairs the Master said "The teleport device, in case you thought I'd forgotten", she withdrew it from a pocket and tossed it to him

He caught it and said "And now Martha Jones, kneel" she did as she was told "And now, beneath us two hundred thousand ships, set to burn across the universe" he grinned turning to a communication device and asked "Are we ready?"

"Awaiting your order" the voice responded while the Master turned to his watch "Three minutes to align the black hole converters, counting down" turning to the clock to see it counting down from 180

"I could never resist a ticking clock" he said with a big smile before shouting out "My children are you ready?" he asked the Toclafane who replied "We are flying, blaze and slice" and repeated it again and again a few times

The Master then turned to face the main deck again "At zero to mark this day, the child Martha Jones will die. My first blood" he chuckled "Any last words?" he asked she just remained silent "Nothing" he said and turned to the Doctor

"Such a disappointment this one Doctor" he said "You had companions who could absorb the Time Vortex this ones useless" and he went to draw his laser screwdriver

But his pocket was empty

That was when two separate plans were activated

Martha explained what she had being doing and the Doctor healed himself using the human race's combined mental power focused through the Archangel Network while Rani sent a command through her PDA

All over the world while the people chanted "Doctor" the Toclafane fell from the sky and their inner works were disabled by the Rani gaining access to their combined neural net and Lucy walking to Rani's side pulling out from behind her back the Master's laser screwdriver while the Master looked on in betrayal

Rani grinned "You really shouldn't have left me with her so long" and Lucy smiled a very sane smile

"She used her psychic powers to correct the chemical imbalance in my brain that caused my madness, once I came too she told me what to do" Lucy explained while Master suddenly cowered against the wall from the Doctor saying "I forgive you"

The Doctor turned to face Jack and said "Captain the paradox machine" and he nodded gathering the soldiers on deck to race and disable the machine

The Master secretly went for the vortex manipulator and disappeared as the Doctor dived to stop him going with him

Jack rushed to the Tardis and shot the paradox machine.

And then the _Valiant_ began to shake

* * *

On the main deck everyone clung to whatever they could as temporal waves hit the flying aircraft carrier. Martha went backwards towards the stairs only to land in the Doctor's arms.

The Doctor didn't waste time and kissed Martha deeply on the lips. Her surprise didn't last long and she started kissing back before the Doctor brought the kiss and told her while holding her close

"Martha I love you, I'm sorry I didn't say it earlier. I was afraid of losing you the way I lost everyone else" he said and her shock was soon replaced by a warm smile

"You'll always have me" she said and they kissed again as the world changed around the _Valiant_.

Rani grinned and shouted to everyone "Hold on to something, time is reversing"

The ravages of what the Master had done to the world started disappearing as time went backwards

After a short while the shaking stopped and the Earth reversed itself one year

While no-one noticed the Master grabbed a pistol that a guard had dropped during the shaking and aimed it at Martha, pulling the trigger.

The kiss abruptly stopped as Martha felt a bullet hit her, the guards quickly took aim and shot the Master, who smiled knowing that he had managed to hurt the Doctor one last time, before life left his body.

Martha felt to the floor as the Doctor held her and her family rushed to her side.

"No…No, I won't lose you" The Doctor said holding Martha close while the Rani grabbed a syringe from out of her pocket and moved quickly to them

"Listen" she told them quickly "I can save her, but she will have to give up being human, become a Timelord like us"

"Is there no other way?" Francine Jones asked and Rani shook her head

"There will be great pain, but it is the only way she can survive. And this choice has to be made now" they all turned to Martha who nodded her head

Rani put the syringe to Martha's arm and injected her

* * *

_Two days later…_

The Doctor and the Rani were in the Doctor's Tardis, undoing the damage that the Master had done; they had personally burnt the body and made the decision to cast everything that remained into a black hole. They could not risk him returning.

"What will you do now?" The Doctor asked

"Well I can hardly go gallivanting across the universe when I have 200 babies on the way can I? UNIT has agreed to give me sanctuary in exchange for my scientific help, besides Miles, Sally and Lucy decided to stick around. Lucy and Sally need to learn more about being a Timelord or Lady in their case, and Miles doesn't have anywhere left to go. His family were already dead before the Master turned on the Paradox machine, the Master was just playing with him"

"How's Martha doing?" Rani asked, finishing her repairs to the circuits under the grating

"Ok, she's still having trouble with having two hearts but everything else seems ok" The Doctor said while he repaired the centre column

"So what are you going to do now?" Rani asked

"Me and Martha are going to travel a bit more, see how it goes" The Doctor said

"Kinda cosy, just the two of you" Rani commented

"Well Jack decided to go back to Cardiff with his team" The Doctor said

Rani smiled a knowing smile "Well I left them a little surprise when they get back to the hub"

The Doctor looked confused "What surprise?"

"Wait and see" Rani said cryptically with a smile

* * *

The four Torchwood 3 personnel entered the tunnel leading into the hub, when Jack noticed a letter stuck to it, addressed to him.

They all looked at him as he opened it as read it out loud

"_Dear Jack_

_It seems your team has been left a woman down, so I thought the least I could do is give you a replacement-"_

Jack looked up and dashed into the hub to see on the sofa under the 'TORCHWOOD' writing on the wall

Gwen Cooper sleeping

Jack turned back to the letter

"_-there was enough clone fluid left from the time babies to create one last clone. So I took the DNA that makes up my appearance and cloned a replica of my own body. But this one is human and using the chameleon arch I gave her the life, knowledge and general personality of Gwen Cooper. _

_Hope you like her_

_Rani_

_P.S. This Gwen doesn't have a relationship with Rhys Williams" _

Jack looked from the letter to the Gwen on the sofa and gently shook her awake

Her brown eyes opened slowly and she looked at them with sleep filled eyes "Morning guys, why are you all looking at me like that?" she asked waking up a bit more

They all smiled and Jack assured her taking her small hand in his "Nothing Gwen nothing"

* * *

_Please Review_


	10. Interlude

_I do not own Doctor Who_

**Interlude – Into the Future**

The streets of Cardiff were empty at five o'clock in the morning, which was why Rani had chosen today to get her Tardis back. Dressed in a fitted black leather jacket, red silk t-shirt, tight black jeans and topped off with heeled knee high black boots. She had looked at the clothes she's chosen and remarked "Earth's fashions have certainly improved"

She walked close to the parking garage close to where her human persona's flat was, where her clone was right now. She withdrew a small gadget from her coat pocket which disabled the security cameras, she didn't want to appear on CCTV and raise some unwanted questions as to why Gwen Cooper was in two places at once.

She approached her human persona's car and withdrew a skeleton key she'd made and used it to unlock the door. She climbed in and shut the door.

Once she locked the car door she removed the air vent on the driver's side door and pressed her finger on the top of the small vent.

There was a moment were nothing happened but then the car's insides began to be distorted by waves of light passing around Rani who sat calmly in the centre of the storm

Rani closed her eyes and when she opened them, she saw the control room of her Tardis.

Her control room was very different to the Doctor's. It resembled a chestnut panelled laboratory, with comfortable large chairs and tables piled with ordered notes and scattered scientific equipment. There was no ceiling as such, but rather a 3D display of this galaxy, which would change to resemble whatever galaxy she was in.

The way she had hidden her Tardis was an invention of hers that she liked to refer to as the Advanced Camouflage Unit, unlike a normal chameleon circuit which changed the outside of the Tardis to resemble something else, the advanced unit could literally turn the Tardis into something else on the outside while the inside remained intact and the only way to deactivate the unit was to trip the system with an ID scanner concealed in the object. Designed to be a means of hiding a Tardis for an extended period of time with a reduced chance of getting discovered

Rani moved to the centre console where she started to start up the main systems, and opened the engines to get some more fuel. Once the engines were warmed up she set the co-ordinates and started her up.

* * *

With the difference of a few seconds Rani's Tardis reappeared in UNIT HQ in London, now shaped as a large cabinet.

Miles, Sally and Lucy who were all waiting in the room stood up at the sudden appearance and waited

Rani appeared from out of the door and said to them "Expecting someone else?" with a smile at Miles, who had never seen a Tardis before and startled at its sudden appearance

She opened the door wide and stood clear to let her three charges enter the Tardis, their reactions to the great insides were vastly different

Lucy had been in the Doctor's Tardis and explored some of the Type 40 he favoured so she showed the same curiosity that one might have viewing a new house

Sally had also see the Doctor's Tardis but had only seen his coral based control room so to seeing the grandness of the Rani's had her astonished

But Miles had the greatest reaction of all, his jaw dropped as he saw the interior of the Tardis and he had to hit on the back by Sally before he remembered to breathe

"Well then" Rani said, closing the door now that they had been ushered inside and moving to the controls

"What are doing?" Lucy asked

"Well I thought we take a little trip" Rani said

Miles asked "What about the timebabies?" while he thought 'She can't mean to leave them behind'

"Well I made a little side trip before coming here and materialised my Tardis around the pods, they're stored in a holding bay onboard" Rani reassured him

"So where are we going?" Sally said excited she had never travelled in time before and was eager to see what was out there

"Late twenty second century" Rani said as she pulled a level that started the centre column moving

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Just an interlude for the moment, chapter is forthcoming

_The Rani's Control room is inspired by the 1996 8__th__ Doctor Movie control room_


	11. Chapter 11

_I do not own Doctor Who _

_To anyone who might be confused Prodigy's Journey and Now there are three are completely separate stories _

**Chapter 10 – Unstable Future **

Rani's Tardis dematerialised in London in the year 2171, four years after the Doctor had left Susan on this world. London was the centre of the UK before the Daleks invaded and it was the centre now that it was rebuilding.

Rani exited the Tardis followed by Miles, Sally and Lucy. They all looked at ruined city and sorrow at how many had died, but then the sunlight revealed in its golden light the building work and people bustling about a marketplace…life...life beginning again anew.

There was hope in the air, people going at their daily lives with vigour.

All four of the Tardis crew dressed in the simple tunics and trousers of time, walked through the streets and looked at the sights around them, reflecting on the human spirit to survive…it was as the Doctor had said indomitable

So Rani started asking questions about Susan, hoping to find some trace of her, after that came to a dead end she started to ask about David Campbell. She had pressed the Doctor and found out the name of the man that Susan had become attached to when the Doctor had been here so maybe he could help them find Susan.

Eventually she discovered that David Campbell was the city's law man, effectively the sheriff of London and that he could often be found at the Old Bailey where he had made his headquarters. So Rani and her crew travelled to the centre of law and order to seek answers.

* * *

They were barred from entering the Old Bailey by deputies and Rani stood up to the leader of the group that blocked their path

"I wish to speak to David Campbell, it is about Susan Foreman" Rani said to him and guard suddenly became very serious

"You had better come inside" the older man complete with iron grey beard and thinning hair said and he led them inside, through corridors, up stairs to the office where David Campbell had set himself up

The door opened to reveal a reasonably well build man whose dark hair had begun to grey prematurely from the pressures of the world on his desk there was a picture of Susan more or less as she had been when Rani had last seen her

David Campbell turned to Rani and asked "You said you knew something Susan please tell me" with an almost desperate look on his face

"I'm her aunt" she lied couldn't go saying she was her grandmother when they looked so much closer in age "I' am looking for her"

David's face fell into depression "Well I' am sorry to disappoint you but Susan was taken by the Followers of Hekic almost two months ago"

"Who?" Rani asked while the natives to this time looked at her incredulously

"I'm not in the mood for games. Show them out Paul" David told his underling who moved to usher them out but Rani went up to David and said quietly so only he could hear

"I know that you saw the Tardis dematerialize, you know who we are" in a firm tone that put him back a step

"No never mind Paul let them stay" David told his man who reluctantly backed off

* * *

Twenty minutes later they all sat in a cluster of seats near the window (except Paul who had been excused to deal with the trial of a thief he had caught)

"Ok start at the beginning" Rani told David

"Well the cult 'The Followers of Hekic' had been around since before the invasion but after it grew 100 fold. Provided answers to those who were looking, they sacrifice people to appease their god Hekic and they just take what they want. I don't know how they found out the Susan was an alien but they did, one night a got home and our place was in tatters. They left a note saying that they had been behind it and that they were going to sacrifice her on the eve of the Summer Solstice…two days from now" David said tears leaking from his eyes

"Any leads?" Sally asked putting her arm around the older man's shoulder

"Nothing" he said back leaning in to Sally, tears flowing freely now as he sobbed

Rani watched the scene with concern her thoughts echoed back to the fact that Susan was to be sacrificed and although she would likely regenerate if both her hearts where destroyed or her whole body was then she would die permanently

"Give me the note and if possible a written copy of their beliefs. I'll see what I can do" Rani told them praying that she wasn't too late

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Please Review


	12. Chapter 12

_I do not own Doctor Who_

**Chapter 11 – Tragic new beginnings…**

Some hours past but Rani had yet to emerge from her lab in her Tardis, assembling the clues that they had

David had followed her and her posse back to the Tardis where they let him inside and he marvelled at its splendid interior and said that they world they come from must be truly wondrous indeed, Rani when she had heard that she fell into a sorrowful silence. She was not relishing the idea of having to tell Susan what had happened to Gallifrey and the part she had played.

She and the Doctor both found out about the 'Ultimate Sanction', the plan to wipe out all reality to ascend to beings of pure consciousness. The way the war had been turning and the plan of the now mad Timelords had left them and a small group of still sane Timelords to come up with their own plan to save all of time, to lock the war in a time lock forever. She devised the plan and the means herself and taught them to the Doctor who at wars end had had no option to deploy them on his own. While she and he had escaped the rest of their allies had been trapped on Gallifrey and their faces haunted both her and the Doctor everyday

But with the new treatment and Susan there was hope that maybe the Timelords would be reborn as they were before, watchers and sometimes guardians of the universe

She had within a few hours decoded the note, it was made of a special paper made only in the Coastolo Islands and there were traces of ash from a volcano that was on the largest island Mildrosa. The islands were formed in the early part of the 22nd Century when a chain of underwater volcanoes erupted and formed a new group of islands in the Mediterranean. Due to their rocky state they had largely left alone as they were unfit for habitation. But after the invasion of the Daleks, a group of scientists using captured Dalek technology to create a viable eco system on the islands and started a community there.

But there were still places on the islands where humans did not venture like the peak of the volcano so it was the likely that it was the place.

Rani walked out of her lab with the single minded purpose, getting her granddaughter back; there was no emotion behind it, just the focus on that task. Her eyes gained a kind of fire, the eternal flame of cold hard power that only really old and powerful beings could attain, the intenseness of the gaze put others back a step as an instinctive fear from the core of their being gripped them.

When she came into the control room to meet her crew of Miles, Sally and Lucy, with David as their guest, they all saw the look in her eyes and tensed

Rani walked to the control console and set the coordinates

No-one said a word

* * *

Rani's Tardis soon landed seconds later and Rani pulled out a box from the draw on her console, she opened it and inside was five laser pistols

She took one at a time and tossed one to each of them, keeping the last for herself

"Right" she said presenting the pistol "The pistol has a stun and kill setting, the default setting is stun, if you need to change it flip the switch on the end of the barrel" she indicated the switch in question

"Now" Rani said before anyone could ask a question "Let's go get Susan"

She walked towards the door of her Tardis, the others following nervously in her wake

* * *

A cultist was meditating at the edge of Volcano ravine when he heard the sound of a great wind; he turned quickly to see what appeared to be a large rock form out of thin air. He stared at the rock for a few minutes before the entrance opened and white light beamed

He shielded his eyes from the strong light while a figure appeared, framed by the light

But before the cultist could make out any features of the figure, he felt something hit him in the chest, like a tennis ball hit him, before his mind exploded in a rush of sound and he fell into unconsciousness

* * *

An hour later the cultists were largely beaten, lying unconscious and bound all over the place. The few that remained were scattered but the cult leader was still uncounted for, and Susan

Rani had separated from her team and made her way to the edge of the top of the volcano. The volcano's lava was although hot was not showing any abnormal activate, staying in a relative state of dormancy but still could easily erupt

The Cult Leader was standing on the edge nearby with a bound and gagged figure at his feet. The short dark bob of hair and the pixie like looks which she could make out as she got closer, it was Susan alright

The Cult leader was about the kick Susan into the lava, Rani ran towards them and judged the distance, they were out of range of her pistol and there was not way she could reach them in time.

* * *

David had just reached the top of the lava pit edge and was much nearer to the leader, he saw the leader about to kick Susan into the pit and time seemed to stop as terror grabbed his soul

Moments flashed before his eyes, the way he and Susan had met, the adventures they had, the good times, the bad times, but always her smiling face filled him with sun light.

In that same second he began to move without thinking, running straight at the cult leader.

He tackled the masked man clad in his rich red and gold robes, sending them tumbling into the fiery pit, his thoughts as he fell were

'I love you my Susan'

* * *

Both Rani and Susan saw David tackle the cult leader and fall into the pit

Susan yelled "DAVID!" as she saw him fall; Rani ran up to her Granddaughter and pulled her into her arms and rocked her slowly as tears poured from Susan's eyes and from her came sounds of anguished cries

Susan felt like her heart had been ripped out and sobbed, the comforting arms around her rocked her gently and made soothing sounds

She stopped sobbing after ten minutes and looked up, the eyes told her exactly who it was

"Grandmother"

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Hope you enjoy reading it, please review and let me know what its like


	13. Chapter 13

**Author's Note **

I have decided to continue the story with a sequel set during The End of Time with a chapter at the beginning to explain what has happened in between the two parts

The reason for this is although I have more time now I still can't commit to writing very much so rather than write chapters which will take time to connect the two points of the story I will write an explanation chapter and then move on to the more exciting stuff

The sequel will be put up the same time as this note


End file.
